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Detailed information for vg1126531677:

Variant ID: vg1126531677 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26531677
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CCGCTACATCGTCTTCGAGGTCAACTCCATCTACACCACATTGCGGTCGCATCGTCCCCGATGCATGCGCCCTTCTCCCCGTCGCTCGCCGCTGCCAAGC[A/T]
TCTTGTTGGCTGCCAGCCTTCTCCCCACCCATCGCCAGGCGCCATCGTCGGGCTTCTACCTACCACCGCCGCCCAACGACTGCCACCCTTCTCCCTGCTG

Reverse complement sequence

CAGCAGGGAGAAGGGTGGCAGTCGTTGGGCGGCGGTGGTAGGTAGAAGCCCGACGATGGCGCCTGGCGATGGGTGGGGAGAAGGCTGGCAGCCAACAAGA[T/A]
GCTTGGCAGCGGCGAGCGACGGGGAGAAGGGCGCATGCATCGGGGACGATGCGACCGCAATGTGGTGTAGATGGAGTTGACCTCGAAGACGATGTAGCGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.80% 17.10% 0.06% 0.00% NA
All Indica  2759 79.20% 20.70% 0.11% 0.00% NA
All Japonica  1512 87.50% 12.50% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 57.80% 42.00% 0.17% 0.00% NA
Indica II  465 80.90% 18.70% 0.43% 0.00% NA
Indica III  913 89.80% 10.20% 0.00% 0.00% NA
Indica Intermediate  786 82.10% 17.90% 0.00% 0.00% NA
Temperate Japonica  767 82.00% 18.00% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 90.50% 9.50% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126531677 A -> T LOC_Os11g43934.1 upstream_gene_variant ; 671.0bp to feature; MODIFIER silent_mutation Average:84.188; most accessible tissue: Minghui63 flag leaf, score: 92.636 N N N N
vg1126531677 A -> T LOC_Os11g43934.2 upstream_gene_variant ; 701.0bp to feature; MODIFIER silent_mutation Average:84.188; most accessible tissue: Minghui63 flag leaf, score: 92.636 N N N N
vg1126531677 A -> T LOC_Os11g43934-LOC_Os11g43950 intergenic_region ; MODIFIER silent_mutation Average:84.188; most accessible tissue: Minghui63 flag leaf, score: 92.636 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1126531677 A T -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126531677 NA 3.97E-11 mr1191 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 2.18E-08 1.13E-12 mr1191 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 8.28E-06 mr1561 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 5.32E-11 mr1644 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 7.96E-08 5.12E-13 mr1644 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 1.00E-11 3.45E-23 mr1191_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 1.05E-13 7.35E-22 mr1191_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 6.06E-06 mr1380_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 8.98E-07 mr1380_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 6.43E-06 mr1561_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 3.64E-06 mr1561_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 2.17E-07 mr1745_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 2.18E-06 mr1875_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 8.60E-06 mr1908_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126531677 NA 3.94E-06 mr1996_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251